Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics

(2014) Adrian WR Serohijos et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Nonclassical antifolates, part 5. Benzodiazepine analogs as a new class of DHFR inhibitors: Synthesis, antitumor testing and molecular modeling study

(2014) Hussein I. El-Subbagh et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO

(2014) Romain A. Studer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solvent environments significantly affect the enzymatic function of Escherichia coli dihydrofolate reductase: Comparison of wild-type protein and active-site mutant D27E

(2013) Eiji Ohmae et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Improving the thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 using a computationally aided method

(2012) Jian Tian et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Protein Quality Control Acts on Folding Intermediates to Shape the Effects of Mutations on Organismal Fitness

(2012) Shimon Bershtein et al.   MOLECULAR CELL

Assessing Predictors of Changes in Protein Stability upon Mutation Using Self-Consistency

(2012) Grant Thiltgen et al.   PLoS One

Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations

(2012) S. Bershtein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy

(2012) Pietro Alfarano et al.   PROTEIN SCIENCE

The interface of protein structure, protein biophysics, and molecular evolution

(2012) David A. Liberles et al.   PROTEIN SCIENCE

Achieving Diversity in the Face of Constraints: Lessons from Metabolism

(2012) R. Milo et al.   SCIENCE

Genetic Draft and Quasi-Neutrality in Large Facultatively Sexual Populations

(2011) R. A. Neher et al.   GENETICS

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

(2011) A. J. Adamczyk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential

(2011) Jiabin Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Performance of protein stability predictors

(2010) Sofia Khan et al.   HUMAN MUTATION

Multiple Global Suppressors of Protein Stability Defects Facilitate the Evolution of Extended-Spectrum TEM β-Lactamases

(2010) Nicholas G. Brown et al.   JOURNAL OF MOLECULAR BIOLOGY

Iterative Saturation Mutagenesis Accelerates Laboratory Evolution of Enzyme Stereoselectivity: Rigorous Comparison with Traditional Methods

(2010) Manfred T. Reetz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein aggregation diseases: pathogenicity and therapeutic perspectives

(2010) Adriano Aguzzi et al.   NATURE REVIEWS DRUG DISCOVERY

Insights into protein folding mechanisms from large scale analysis of mutational effects

(2010) A. N. Naganathan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design and analysis of synthetic carbon fixation pathways

(2010) A. Bar-Even et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dry molten globule intermediates and the mechanism of protein unfolding

(2010) Robert L. Baldwin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Exploring protein fitness landscapes by directed evolution

(2009) Philip A. Romero et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Design of therapeutic proteins with enhanced stability

(2009) N. Chennamsetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Helix propensities calculations for amino acids in alanine based peptides using Jarzynski's equality

(2009) Ignacia Echeverria et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation

(2009) Ville Mustonen et al.   TRENDS IN GENETICS

FitSpace Explorer: An algorithm to evaluate multidimensional parameter space in fitting kinetic data

(2008) Kenneth A. Johnson et al.   ANALYTICAL BIOCHEMISTRY

Amyloid formation by globular proteins under native conditions

(2008) Fabrizio Chiti et al.   Nature Chemical Biology

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

Universality and diversity of folding mechanics for three-helix bundle proteins

(2008) J. S. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA